Abstract: Cyanobacteria are well recognized for their ability to fix atmospheric nitrogen. This group holds significant as a major natural food source for cultural forms. But, a significant number of them are also known for their nuisance value on account of their ability to produce potentially lethal toxins. The population density of Microcystis aeruginosa accounts for bloom like situation in fish culture ponds. The population density of M. aeruginosa was found to be maximum in HP, followed by DP and MP. Bloom like situation was recorded during summer and was observed only when its population density was > 2.5x104cells/cm3. Ochromonas danica, a golden brown Chrysophytean alga engulfs and digests Microcystis aeruginosa colonies, a situation observed during survey of MP, when water sample was examined microscopically. The population density of M. aeruginosa in BRL-III medium inoculated with different concentration of culture suspension of Ochromonas danica was studied. In vitro results related to biological control indicated that a population density of 9.9 x 104 cells/cm3 (1.5 ml) to 16.5 x 104 cells/cm3 (2.5 ml) of O. danica caused a rapid decline in the population density of M. aeruginosa to almost nil only after 6 or 9 days of incubation. Investigations related to growth response of toxic strains of M. aeruginosa in BRL-III medium supplemented with different concentrations of Copper sulphate, Potassium permaganate, Quinine, Urea, KMnO4, Ammonia, Simazine, Calcium hypochlorite, Ferric alum and Cupricide indicated that CuSO4, KMnO4 and Quinine were more toxic to M. aeruginosa in comparison to urea and ammonia. Copper sulphate and potassium permagnate caused a rapid decline in population density of M. aeruginosa to almost nil following 15 days of incubation; the same concentration of quinone brings this effect within 6 days. Quinones was more toxic to Microcystis aeruginosa followed by copper sulphate, potassium permagnate, urea and ammonia. Among calcium hypochlorite, ferric alum and cupricide, calcium hypochlorite showed maximum inhibitory effect on the growth of M. aeruginosa.